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| Status |
Public on Mar 13, 2010 |
| Title |
Mitochondrial and nuclear genomic response to loss of LRPPRC expression |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Rapid advances in genotyping and sequencing technology have dramatically accelerated the discovery of genes underlying human disease. Elucidating the function of such genes and understanding their role in pathogenesis, however, remains challenging. Here, we introduce a genomic strategy to functionally characterize such genes, and apply it to LRPPRC (leucine-rich PPR-motif containing), a poorly studied gene that is mutated in Leigh Syndrome, French Canadian type (LSFC).
We utilize RNAi to engineer an allelic series of cellular models in which LRPPRC has been stably silenced to different levels of knockdown efficiency. Using expression profiling, we discovered a specific role for LRPPRC in the expression of all mitochondrial DNA (mtDNA)-encoded mRNAs, but not the rRNAs, without affecting nuclear genes encoding mitochondrial proteins.
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| Overall design |
We designed seven shRNAs targeting the LRPPRC cDNA sequence to silence its expression in MCH58 immortalized human fibroblasts. The LRPPRC expression level in these cells ranged from 9% to 100%. We demonstrated that knockdown cells carried stable silencing of the target gene and associated biochemical phenotypes. Our goal was to engineer stable knockdown cells which recapitulate the LSFC disease phenotype and subject them to expression profiling using Affymetric microarrays to identify genesets and biochemical pathways that are altered.
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| Contributor(s) |
Gohil VM, Mootha VK |
| Citation(s) |
20220140 |
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| Submission date |
Mar 11, 2010 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Vishal M Gohil |
| Organization name |
Massachusetts General Hospital
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| Department |
Center for Human Genetic Research
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| Lab |
Vamsi K Mootha
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| Street address |
185 Cambridge Street
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
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| Platforms (1) |
| GPL570 |
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array |
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| Samples (14)
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| GSM521268 |
LRPPRC knockdown1, biological replicate 1 |
| GSM521269 |
LRPPRC knockdown1, biological replicate 2 |
| GSM521270 |
LRPPRC knockdown2, biological replicate 1 |
| GSM521271 |
LRPPRC knockdown2, biological replicate 2 |
| GSM521272 |
LRPPRC knockdown3, biological replicate 1 |
| GSM521273 |
LRPPRC knockdown3, biological replicate 2 |
| GSM521274 |
LRPPRC knockdown4, biological replicate 1 |
| GSM521275 |
LRPPRC knockdown4, biological replicate 2 |
| GSM521276 |
LRPPRC knockdown5, biological replicate 1 |
| GSM521277 |
LRPPRC knockdown5, biological replicate 2 |
| GSM521278 |
LRPPRC knockdown6, biological replicate 1 |
| GSM521279 |
LRPPRC knockdown6, biological replicate 2 |
| GSM521280 |
LRPPRC knockdown7, biological replicate 1 |
| GSM521281 |
LRPPRC knockdown7, biological replicate 2 |
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| Relations |
| BioProject |
PRJNA124753 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE20847_RAW.tar |
64.4 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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